Dear gmx users
I did some simulations of multimers (peptides) in rhombic dodecahedron
boxes. In the initial configuration of the system, the peptides are
close of each other in the center of the box.
My aim to see if the peptides do aggregate during the trajectory or if
they tend to stay apart. A rough estimate can be taken from the gyration
radius for all the peptides together.
Already did a trjconv -pbc nojump pre-treatment on the trajectory,
before calculating the Rgyr. The gyration.xvg plots sometimes do show
abrupt jumps, and this is surely due to boundary effects, if I correctly
understood the PBC idea. If a peptide approaches the boundary, it
appears on the opposite side, thus rgyr will show a false sudden
increase. In fact, the peptide could be closer to the rest of the other
peptide molecule(s).
Thus my question is:
how to deal with peptide clusters that span over the periodic boundaries?
A similar question was done by Singh:
http://www.gromacs.org/pipermail/gmx-users/2007-January/025474.html
and it was suggested by Chris Neale to pre-process the trajectory (see
http://www.gromacs.org/pipermail/gmx-users/2007-January/025481.html) with:
trjconv -f a.xtc -o a_cluster.gro -e 0.001 -pbc cluster
grompp -f a.mdp -c a_cluster.gro -o a_cluster.tpr
trjconv -f a.xtc -o a_cluster.xtc -s a_cluster.tpr -pbc nojump
but I'm getting infinite loops on the -pbc cluster treatment, same as reported by Chris
(http://www.gromacs.org/pipermail/gmx-users/2008-July/035343.html).
Best,
Léon